Aided by high-throughput sequencing technology, plant biologists have identified large numbers of novel open reading frames (ORFs). Large-scale functional genomic approaches are needed in order to convert this sequence information into functional information. Traditionally, Agrobacterium Ti plasmid transfer DNA (T-DNA) and transposon-based insertional mutant populations have provided the resources for the analysis of phenotypes. Large collections of such insertion and deletion mutant populations have been generated for plants like Arabidopsis thaliana due to the ease of transformation. However, these mutant collections are not generally saturated, meaning that all ORFs have not been disrupted or tagged by an insertion or deletion. Saturation may be difficult to achieve because of bias in the insertion of T-DNA or transposons and because disruptions of essential genes often result in nonviable plants that are lost from the collection. In addition, many plant genomes have a high degree of gene duplication, and therefore a disruption of a gene will not yield any measurable phenotype because a duplicate copy of the gene compensates for the defect. Alternative methods for probing gene function have been developed, including dsRNA-mediated suppression of genes by vectors that produce sense and antisense transcripts. However, all of these approaches rely on the generation of transgenic lines. The generation of transgenic plant lines is a time consuming process, and is only practical for high throughput analyses in Arabidopsis. 
Gene silencing approaches, such as virus induced gene silencing (VIGS), offer an attractive and quick alternative for knocking out expression of a gene without the need to genetically transform the plant. Using this method, recombinant virus carrying a partial sequence of a host gene is used to infect the plant. When the virus spreads systemically, the endogenous gene transcripts, which are homologous to the insert in the viral vector (VIGS-vector), are degraded by post-transcriptional gene silencing (PTGS). Vectors for carrying out gene silencing suffer from a variety of shortcomings, including inability to silence genes in proliferating or non-proliferating cells, inability to silence genes in a large area of the target plant, and poor rate of infection in target plants.
Improved vectors for use in plants, and particularly vectors for use in gene silencing and high-throughput gene analysis, are needed in the field of plant biology.